Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	harmonization_novoalign.cwl	https://github.com/uc-cdis/genomel_pipelines.git Path: genomel/cwl/workflows/harmonization/harmonization_novoalign.cwl Branch/Commit ID: 3657003ce9fafd0e1916914ec5bf5fd3f28aedaf
	sec-wf-out.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/sec-wf-out.cwl Branch/Commit ID: 691dea280b40ac177b4a38b33375139ca0ce7e81
	tt_kmer_compare_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_compare_wnode.cwl Branch/Commit ID: 68058b108cb5b0b72ebe244c42eefa2747e1d64a
	tt_fscr_calls_pass1	https://github.com/ncbi/pgap.git Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: d218e081d8f6a4fdab56a38ce0fc2fae6216cecc
	align_sort_sa	https://github.com/ncbi/pgap.git Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: 093b60e546237c06cfe7820d6ac8d66467e66725
	trim-chipseq-se.cwl Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/trim-chipseq-se.cwl Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
	Pipeline for evaluating differential expression of genes across datasets	https://github.com/hubmapconsortium/rna-data-products.git Path: pipeline.cwl Branch/Commit ID: 93e36d7e6b8ab02f927b2e54fd37db0c14fff93b
	cellpose.cwl	https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git Path: steps/cellpose.cwl Branch/Commit ID: 5b866e480fb557cf53d619a22068c73548e337d5
	bam-bedgraph-bigwig.cwl Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.	https://github.com/datirium/workflows.git Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e
	basename-fields-test.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/basename-fields-test.cwl Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59